1. SiteEngine: Functional Sites Structural Search Engine
Shulman-Peleg A., Nussinov R. and Wolfson H. J. Recognition of Functional Sites in Proteins Structures, J. Mol. Biol. 339(3),

2. SiteEngine
Recognizes surface regions of one protein that resemble a specific binding site of another.
Measures the similarity of physico-chemical and geometrical properties.
SiteEngine
Input
Output
Complete protein
Binding site
3D transfor-mation.
Similarity Score

3. Biological Motivation
Potential ligands and ligand fragments.
Prediction of side effects.
Inferring a function of a novel protein.
Biological classifications.

4. 3-D Database Searches Application III:
Query: a complete protein DB: binding sites
Application I:
Query: a binding site
DB: complete proteins
Application II:
Query: a binding site
DB: binding sites
DB of complete proteins
DB of binding sites

5. - Hydrogen bond acceptor
- Hydrogen bond donor
- donor/acceptor
- Hydrophobic Aliphatic
- Aromatic (PI) contacts
Representation
III. The solid angle shape function (Connolly 83’) is calculated at the center of each physico-chemical patch.
I. Each amino acid is represented by a set of its physico-chemical properties (Schmitt 02’).
II. Each property creates a physico-chemical patch on the protein surface.

6. Recognition of adenine binding sites
A benchmark data set (121 proteins) was searched for binding sites similar to that of cAMP-dependent protein kinase (1atp).
Ranked 7 was the an ATP binding site of a structurally different “hypothetical” protein MJ0577 from Methanococcus jannaschii.
- cAMP-dependent protein kinase (1atp)
- MJ0577 Structural genomics protein (1mjh, ranked 7)
*The ligands are displayed for verification only!

7. Searching the Entire PDB
1. Searching the ASTRAL dataset with the adenine binding site of c-AMP dependent protein kinase (1atp).
Replication factor C (1iqp, purple). Ranked 19.
D-Ala-D-Ala ligase (1iow). Ranked 31.
2. Searching the ASTRAL dataset with the estradiol binding site of sex hormone-binding globulin (1lhu).
Tropinone reductase (2ae2). Ranked 43.
Estrogen sulfotransferase (1aqu). Ranked 38.

8. Web Server

9. Matching Triplets of pseudo-centers are hashed and matched.
Each pair of triangles with similar side lengths and similar nodes defines a candidate transformation.
Hash Table Key = (index, )
Index =
PII
ALI
Transformation
Complexity:

10. Hierarchical Scoring Comparison of the shapes and
physico-chemical properties of
the surfaces.
1. Low-Resolution scoring
Based on a sparse representation by chemically important surface points (centers of physico-chemical surfaces patches).
2. High-Resolution scoring
More precise calculations based on high density sampling of the surfaces.

11. Interacting Triangles
Interacting triangle (I-triangle) is a triplet of functional groups (pseudocenters) of one molecule that is recognized to form three interactions with the other molecule.
- Hydrogen bond acceptor
- Hydrogen bond donor
- Donor/acceptor
- Hydrophobic Aliphatic
- Aromatic (PI) contacts

12. Hashing and Matching of I-triangles

13. Figure 1: SiteEngine Recognition of an ATP binding site similar to that of cAMP-dependent protein kinase (1atp- , ATP- ) in the structure of a Structural Genomics protein MJ0577 (1mjh- , ATP- ).
- Hydrogen bond acceptor
- Hydrogen bond donor
- Donor/acceptor
- Hydrophobic Aliphatic
- Aromatic (PI) contacts
Figure 2: I2I-SiteEngine Alignment of the interfaces formed by Subtilisin Thermitase with Eglin C (3tec) and B-trypsin with BPTI inhibitor (2ptc)

14. Recognition of estradiol binding sites
The benchmark data set (121 proteins) was searched for binding sites similar to that of 1lhu (Sex hormone-binding globulin).
All 12 proteins which are in complex with estradiol (EST) were within the 30 best solutions.
(A)
(B)
proteins from the data set 1qkt (A), 1fds (B). - ligands and active sites (dots) from : 1qkt (A), 1fds (B). - ligand and active site (dots) from 1lhu
(A) – highest ranking (rank 2) EST binding site of 1qkt - estrogen receptor alpha
(B) – lowest ranking (rank 29) EST binding site of 1fds - 17beta hydroxysteroid dehydrogenase
*The ligands are displayed for verification only!